Microbial populations in a full-scale anaerobic digester fed on food waste were monitored over an 18-month period using qPCR. The digester exhibited a highly dynamic environment in which methanogenic populations changed constantly in response to availability of substrates and inhibitors. The methanogenic population in the digester was dominated by Methanosaetaceae, suggesting that aceticlastic methanogenesis was the main route for the production of methane. Sudden losses (69%) in Methanosaetaceae were followed by a build-up of VFAs which were subsequently consumed when populations recovered. A build up of ammonium inhibited Methanosaetaceae and resulted in shifts from acetate to hydrogen utilization. Addition of trace elements and alkalinity when propionate levels were high stimulated microbial growth. Routine monitoring of microbial populations and VFAs provided valuable insights into the complex processes occurring within the digester and could be used to predict digester stability and facilitate digester optimization. (c) 2013 Elsevier Ltd. All rights reserved.